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LINGUIST List 22.977

Mon Feb 28 2011

Calls: Computational Ling/ Journal of Biomedical Informatics (Jrnl)

Editor for this issue: Danniella Hornby <d-hornbyhotmail.com>

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        1.     Kevin Bretonnel Cohen , Journal of Biomedical Informatics

Message 1: Journal of Biomedical Informatics
Date: 03-Feb-2011
From: Kevin Bretonnel Cohen <kevin.cohengmail.com>
Subject: Journal of Biomedical Informatics
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Full Title: Journal of Biomedical Informatics

Linguistic Field(s): Computational Linguistics

Call Deadline: 15-Mar-2011

Journal of Biomedical Informatics
Call for Papers: Mining the Pharmacogenomics Literature
Guest editors: K. Bretonnel Cohen and Russ Altman
Co-editors: Yael Garten, Udo Hahn, Nigam Shah

We are inviting submissions for a special issue of the Journal of
Biomedical Informatics on automatic or semi-automatic extraction of
relationships between biomedical entities relevant to pharmacogenomics from
the research literature. Accepted papers will focus on methods for the
extraction of genotype-phenotype, genotype-drug, and phenotype-drug
relationships and the novel use of these relationships for advancing
pharmacogenomic research. Efforts aimed at creating benchmark corpora as
well as comparative evaluation of existing relationship extraction methods
are of special interest.

The planned special issue aims to address the gap in coverage of text
mining for pharmacogenomics, as an important initial application area of
genomics in clinical medicine, and thus an important translational medicine
activity. The issue is intended to focus particularly on
genotype-phenotype-drug relationships. It will include broad categories of
work that have been well-studied in the past, specifically text mining and
reasoning, but will restrict submissions to applications of that work to
the constrained area of pharmacogenomics, and particularly
genotype-phenotype-drug relationships. Topics that are solicited include:

- Relation extraction between genotypes, phenotypes, and drugs, and other
semantic classes relevant to pharmacogenomics
- Corpus development for pharmacogenomics text mining
- Associating gene variants (mutations, alleles, rs/ss numbers) to the
associated gene name
- Using text mining to extract information about the association of drugs
with clinical phenotpyes
- Use of biological networks in combination with text mining to facilitate
- Work on the corpus of documents linked to by PharmGKB
- Reasoning systems applied over the PharmGKB knowledge base
-Creation of ontologies to help relate molecular action of drugs to their
clinical effects.

Work on gene taggers alone will not be considered. The key feature we seek
is the use of language technologies to understand molecular basis of drug
response, its variability, and its impact on phenotypes at the molecular,
cellular, organ and whole organisms level. Approaches that combine
text-mining and knowledge-based systems are of special interest.

All submissions should follow the guidelines for authors available at the
Journal of Biomedical Informatics web site
(http://www.elsevier.com/locate/yjbin). JBI generally publishes at least
one methodological review paper in each issue, and we would welcome a
review of the state of the art in text mining for pharmacogenomics for this
special issue.

Authors may contact special issue lead editors (kevin.cohengmai.com or
russ.altmanstanford.edu) with a proposed abstract before submission.

Authors must submit their paper via the online Elsevier Editorial System
(EES) at http://ees.elsevier.com/jbi. Authors can register and upload
their text, tables, and figures, as well as subsequent revisions, through
this website. Potential authors may contact the Publishing Services
Coordinator in the journal's editorial office (jbielsevier.com) for
questions regarding this process. When asked for the category of their
submission, they should indicate that it is for the special issue on Mining
the pharmacogenomics literature (which will appear as 'Pharmacogenomics'
on the pull-down menu).

Submission Deadline: March 15, 2011.

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